Variant report

Variant	rs2555442
Chromosome Location	chr2:64489291-64489292
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:64370065..64372798-chr2:64488901..64490869,2	MCF-7	breast:
2	chr2:64430204..64433000-chr2:64488662..64490502,2	MCF-7	breast:
3	chr2:64488028..64492838-chr2:64495770..64499229,4	K562	blood:
4	chr2:64489082..64492227-chr2:64492884..64497005,5	MCF-7	breast:
5	chr2:64488474..64490275-chr2:64553073..64555333,2	K562	blood:
6	chr2:64488099..64490246-chr2:64490970..64494395,3	K562	blood:

Variant related genes	Relation type
ENSG00000225889	Chromatin interaction
ENSG00000197329	Chromatin interaction
ENSG00000230923	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1019685	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs1019686	0.84[CEU][hapmap];0.85[EUR][1000 genomes]
rs1025209	0.86[EUR][1000 genomes]
rs1025210	0.86[EUR][1000 genomes]
rs1365482	0.85[EUR][1000 genomes]
rs1426710	0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1529101	0.85[EUR][1000 genomes]
rs1582792	0.86[EUR][1000 genomes]
rs1816618	0.80[EUR][1000 genomes]
rs2059634	0.85[EUR][1000 genomes]
rs2114432	0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs2247947	0.85[EUR][1000 genomes]
rs2251764	0.96[CEU][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2254856	0.83[ASN][1000 genomes]
rs2555425	0.86[EUR][1000 genomes]
rs2555426	0.86[EUR][1000 genomes]
rs2555434	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs2555436	0.85[EUR][1000 genomes]
rs2555437	0.85[EUR][1000 genomes]
rs2555438	0.85[EUR][1000 genomes]
rs2555441	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2698523	0.85[EUR][1000 genomes]
rs2698526	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2698527	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2698530	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2698541	0.96[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2951018	0.84[EUR][1000 genomes]
rs6750096	0.85[EUR][1000 genomes]
rs869739	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs871776	0.87[CEU][hapmap];0.89[YRI][hapmap];0.84[EUR][1000 genomes]
rs890481	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs890482	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531376	chr2:64094322-64521876	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv1013132	chr2:64235175-64631084	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	esv2757803	chr2:64253005-64539556	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	esv2759055	chr2:64253005-64539556	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv428396	chr2:64253005-64539556	Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
6	esv34698	chr2:64312142-64521366	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	esv34955	chr2:64312182-64521290	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
8	nsv1006553	chr2:64339907-64764771	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
9	nsv9957	chr2:64341714-64518231	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
10	esv13275	chr2:64342247-64515169	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
11	nsv1012905	chr2:64342469-64508983	Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
12	nsv1013735	chr2:64342469-64512286	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
13	esv3693324	chr2:64342469-64513207	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
14	nsv999608	chr2:64342469-64517459	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
15	nsv1000390	chr2:64343861-64512286	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
16	esv2756924	chr2:64349202-64521290	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
17	nsv1004899	chr2:64369300-64513607	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
18	nsv535769	chr2:64369300-64513607	Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
19	nsv1015084	chr2:64369734-64512286	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
20	nsv1005492	chr2:64452441-64588323	Bivalent/Poised TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases
21	nsv834244	chr2:64480943-64646259	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:64484000-64489600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr2:64485800-64489600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
3	chr2:64486000-64489400	Strong transcription	H1 Cell Line	embryonic stem cell
4	chr2:64486000-64491200	Enhancers	Adipose Nuclei	Adipose
5	chr2:64486200-64492600	Enhancers	Fetal Muscle Leg	muscle
6	chr2:64486400-64490000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
7	chr2:64486600-64489600	Strong transcription	iPS-15b Cell Line	embryonic stem cell
8	chr2:64486800-64490000	Weak transcription	Fetal Kidney	kidney
9	chr2:64487000-64489400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr2:64487000-64489400	Weak transcription	NHEK	skin
11	chr2:64487000-64489600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr2:64487000-64490000	Weak transcription	Ovary	ovary
13	chr2:64487000-64490000	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr2:64487000-64490000	Weak transcription	NHDF-Ad	bronchial
15	chr2:64487000-64490200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr2:64487000-64494800	Weak transcription	Fetal Heart	heart
17	chr2:64487000-64495200	Weak transcription	Fetal Lung	lung
18	chr2:64487000-64500000	Weak transcription	Psoas Muscle	Psoas
19	chr2:64487200-64490000	Weak transcription	Brain Angular Gyrus	brain
20	chr2:64487200-64490000	Weak transcription	HSMMtube	muscle
21	chr2:64487200-64491600	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr2:64487200-64491600	Enhancers	Placenta	Placenta
23	chr2:64487200-64491800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr2:64487400-64489400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
25	chr2:64487600-64489400	Enhancers	Liver	Liver
26	chr2:64487600-64489400	Weak transcription	Fetal Muscle Trunk	muscle
27	chr2:64487800-64490200	Enhancers	Duodenum Mucosa	Duodenum
28	chr2:64487800-64490800	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
29	chr2:64487800-64492400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr2:64488000-64490400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr2:64488000-64493000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr2:64488000-64493400	Genic enhancers	ES-I3 Cell Line	embryonic stem cell
33	chr2:64488000-64493400	Genic enhancers	HUES6 Cell Line	embryonic stem cell
34	chr2:64488200-64489600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr2:64488200-64490000	Enhancers	Sigmoid Colon	Sigmoid Colon
36	chr2:64488200-64491800	Genic enhancers	HUES48 Cell Line	embryonic stem cell
37	chr2:64488200-64492200	Enhancers	Primary monocytes fromperipheralblood	blood
38	chr2:64488200-64493600	Genic enhancers	HUES64 Cell Line	embryonic stem cell
39	chr2:64488400-64489400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr2:64488400-64489600	Enhancers	K562	blood
41	chr2:64488400-64489600	Weak transcription	NH-A	brain
42	chr2:64488400-64489800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
43	chr2:64488400-64489800	Enhancers	Primary hematopoietic stem cells short term culture	blood
44	chr2:64488400-64490200	Enhancers	HUVEC	blood vessel
45	chr2:64488400-64490800	Enhancers	Primary B cells from peripheral blood	blood
46	chr2:64488600-64490600	Enhancers	Primary B cells from cord blood	blood
47	chr2:64488800-64489400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr2:64488800-64490000	Weak transcription	GM12878-XiMat	blood
49	chr2:64488800-64490400	Enhancers	Stomach Mucosa	stomach
50	chr2:64488800-64490800	Enhancers	Spleen	Spleen

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